Data

This section illustrates how to access data, and defines helper methods to filter, map, summarise, and plot data.

Once refined, these helper functions will become core wastdr functionality.

Caveat

• The data as shown is still pre-QA until this message disappears.
• Usernames are still hilariously wrong after matching the usernames (as submitted) to the actual usernames in WAStD. See the field commments for QA messages.

Load data

if (file.exists("tracks.Rda")){
    load("tracks.Rda")
} else {
    track_records <- wastdr::wastd_GET("turtle-nest-encounters")
    tracks_all <- parse_turtle_nest_encounters(track_records)
    surveys <- wastd_GET("surveys") %>% parse_surveys()
    save(tracks_all, track_records, surveys, file = "tracks.Rda")
}

Filter data

To filter records to one area, we can either filter by area or site ID (once enabled), or simply filter by a bounding box. Additionaly, we’ll filter by date.

Site names and IDs are only correct at the time of writing. As they could change, please double-check the correct spelling of your own place names and their IDs in WAStD.

filter_2017 <- . %>% dplyr::filter(date > dmy("01/10/2017"), date < dmy("31/03/2018"))
filter_broome <- . %>% dplyr::filter(area_name=="Cable Beach Broome")
filter_broome_sites <- . %>% dplyr::filter(site_id %in% c(22, 23, 24))
filter_cbb1 <- . %>% dplyr::filter(site_name=="Cable Beach Broome Sector 1")
filter_cbb2 <- . %>% dplyr::filter(site_name=="Cable Beach Broome Sector 2")
filter_cbb3 <- . %>% dplyr::filter(site_name=="Cable Beach Broome Sector 3")
filter_eighty_mile_beach <- . %>% dplyr::filter(area_name=="Eighty Mile Beach Caravan Park")
filter_anna_plains <- . %>% dplyr::filter(area_name=="Anna Plains")
filter_port_hedland_sites <- . %>% dplyr::filter(site_id %in% c(35, 45))
filter_port_hedland_cemetery <- . %>% dplyr::filter(site_name=="Port Hedland Cemetery Beach")
filter_port_hedland_prettypool <- . %>% dplyr::filter(site_name=="Port Hedland Pretty Pool Beach")
filter_west_pilbara <- . %>% dplyr::filter(area_name=="West Pilbara Turtle Program beaches Wickam")
filter_delambre <- . %>% dplyr::filter(area_name=="Delambre Island")
filter_rosemary <- . %>% dplyr::filter(area_name=="Rosemary Island")
filter_thevenard <- . %>% dplyr::filter(area_name=="Thevenard Island")

tracks <- tracks_all %>% filter_2017

Summarise and plot data

Data (all tracks or filtered subsets) are filtered to only fresh observations, then grouped and tallied by date, species and type.

Daily summaries are shown in wide form as tables, and (using long form) as timeseries plots.

species_by_type <- . %>% 
  filter(nest_age=="fresh") %>%
  group_by(species, nest_type) %>% 
  tally() %>%
  ungroup() %>% 
  tidyr::spread(nest_type, n, fill=0)

daily_species_by_type <- . %>% 
    filter(nest_age=="fresh") %>%
    group_by(date, species, nest_type) %>% 
    tally() %>%
    ungroup()

daily_summary <- . %>% 
    daily_species_by_type %>% 
    tidyr::spread(nest_type, n, fill=0) %>%
    DT::datatable(.)

tracks_ts <- . %>% 
    daily_species_by_type %>% 
    {ggplot2::ggplot(data=., aes(x = date, y = n, colour = nest_type)) + 
            ggplot2::geom_point() + 
            ggplot2::geom_smooth(method = "auto") +
            # ggplot2::geom_line() +
            ggplot2::scale_x_date(breaks = scales::pretty_breaks(),
                                  labels = scales::date_format("%d %b %Y")) +
            ggplot2::scale_y_continuous(limits = c(0, NA)) +
            ggplot2::xlab("Date") +
            ggplot2::ylab("Number counted per day") +
            ggplot2::ggtitle("Nesting activity") +
            ggplot2::theme_light()}

Nesting activity

This chapter uses the data and helpers from the above section and provides some insight into the different regions.

This section is by no means complete and can be extended as appropriate.

Overall

tracks %>% map_tracks

Broome Cable Beach

tracks_cbb <- tracks %>% filter_broome
tracks_cbb %>% add_nest_labels %>%  map_tracks

tracks_cbb %>% DT::datatable(.)

tracks_cbb %>% daily_summary

tracks_cbb %>% tracks_ts
#> `geom_smooth()` using method = 'loess'

# named_nests_cbb <- tracks_cbb %>% filter(!(is.na(name)))
# named_nests_cbb %>% tracks_map
# named_nests_cbb %>% DT::datatable(.)

surveys_cbb <- surveys %>% filter_broome_sites
place <- "Cable Beach Broome"
surveys_cbb %>% plot_survey_count(place)

surveys_cbb %>% list_survey_count(place)

surveys_cbb %>% plot_survey_effort(place)

surveys_cbb %>% list_survey_effort(place)

surveys_cbb %>% survey_hours_per_person %>% DT::datatable(.)

Anna Plains

tracks_ap <- tracks %>% filter_anna_plains
tracks_ap %>% map_tracks

tracks_ap %>% DT::datatable(.)

tracks_ap %>% daily_summary

tracks_ap %>% tracks_ts
#> `geom_smooth()` using method = 'loess'

Eighty Mile Beach

tracks_emb <- tracks %>% filter_eighty_mile_beach
tracks_emb %>% map_tracks

tracks_emb %>% DT::datatable(.)

tracks_emb %>% daily_summary

tracks_emb %>% tracks_ts
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17496
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 7.05
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 2.3619e-17
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 49.702
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used
#> at 17496
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius
#> 7.05
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal
#> condition number 2.3619e-17
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : There are other
#> near singularities as well. 49.702

Port Hedland

tracks_pth_cem <- tracks %>% filter_port_hedland_cemetery
tracks_pth_ppo <- tracks %>% filter_port_hedland_prettypool

tracks_pth_cem %>% map_tracks

tracks_pth_cem %>% DT::datatable(.)

tracks_pth_cem %>% daily_summary

tracks_pth_cem %>% tracks_ts %T>% ggsave(filename="~/pth_daily_tracks_cem.png", device="png", width=9, height=5)
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : span too small. fewer data values than degrees of freedom.
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17476
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17476
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 0.185
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 1
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17513
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger

#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger
#> Warning: Computation failed in `stat_smooth()`:
#> NA/NaN/Inf in foreign function call (arg 5)
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : span too small. fewer data values than degrees of freedom.
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17476
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17476
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 0.185
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 1
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17513
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 0.034225
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger

#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger
#> Warning: Computation failed in `stat_smooth()`:
#> NA/NaN/Inf in foreign function call (arg 5)

tracks_pth_ppo %>% map_tracks

tracks_pth_ppo %>% DT::datatable(.)

tracks_pth_ppo %>% daily_summary

tracks_pth_ppo %>% tracks_ts %T>% ggsave(filename="~/pth_daily_tracks_ppo.png", device="png", width=9, height=5)
#> `geom_smooth()` using method = 'loess'
#> `geom_smooth()` using method = 'loess'

surveys_pth <- surveys %>% filter_port_hedland_sites
place <- "Port Hedland"
surveys_pth %>% plot_survey_count(place)

surveys_pth %>% list_survey_count(place)

surveys_pth %>% plot_survey_effort(place)

surveys_pth %>% list_survey_effort(place)

# named_nests_pth <- tracks_pth %>% filter(!(is.na(name)))
# named_nests_pth %>% map_tracks
# named_nests_pth %>% DT::datatable(.)

West Pilbara Turtle Program

tracks_wp <- tracks %>% filter_west_pilbara
tracks_wp %>% map_tracks

tracks_wp %>% DT::datatable(.)

tracks_wp %>% daily_summary

tracks_wp %>% tracks_ts
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : span too small. fewer data values than degrees of freedom.
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17494
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 14.275
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 0
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 1703.6
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : span too small.
#> fewer data values than degrees of freedom.
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used
#> at 17494
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius
#> 14.275
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal
#> condition number 0
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : There are other
#> near singularities as well. 1703.6

Delambre Island

tracks_de <- tracks %>% filter_delambre
tracks_de %>% map_tracks

tracks_de %>% DT::datatable(.)

tracks_de %>% daily_summary

tracks_de %>% tracks_ts
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : span too small. fewer data values than degrees of freedom.
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17508
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 3.27
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 0
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 2628.6
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : span too small.
#> fewer data values than degrees of freedom.
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used
#> at 17508
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius
#> 3.27
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal
#> condition number 0
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : There are other
#> near singularities as well. 2628.6
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17510
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 2
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 5.1026e-17
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 4
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used
#> at 17510
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius
#> 2
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal
#> condition number 5.1026e-17
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : There are other
#> near singularities as well. 4
#> Warning: Removed 104 rows containing missing values (geom_smooth).

Rosemary Island

Data pending upload from tablets.

tracks_ri <- tracks %>% filter_rosemary
tracks_ri %>% map_tracks
tracks_ri %>% DT::datatable(.)
tracks_ri %>% daily_summary
tracks_ri %>% tracks_ts

Thevenard Island

tracks_thv <- tracks %>% filter_thevenard
tracks_thv %>% map_tracks

tracks_thv %>% DT::datatable(.)
#> Warning in instance$preRenderHook(instance): It seems your data is too
#> big for client-side DataTables. You may consider server-side processing:
#> http://rstudio.github.io/DT/server.html

tracks_thv %>% daily_summary

tracks_thv %>% tracks_ts
#> `geom_smooth()` using method = 'loess'
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : span too small. fewer data values than degrees of freedom.
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17506
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 2.5e-05
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 17506
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 0.005
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 1
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : at 17507
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : radius 2.5e-05
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : all data on boundary of neighborhood. make span bigger
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : There are other near singularities as well. 2.5e-05
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger

#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : zero-width neighborhood. make span bigger
#> Warning: Computation failed in `stat_smooth()`:
#> NA/NaN/Inf in foreign function call (arg 5)